[gmx-users] MD of DNA-protein complex AND non-protein inhibitor

[jlenz]

dear gromacs users,

i used gromacs calculate MD trajectories of protein and DNA  
covalently linked. to do so i applied the AMBER ff ports.
afterwards i used a molecular docking tool to dock small non-protein  
ligands into potential cavities built of the DNA-protein complex.
now i am facing the problem, that i again want to simulate the  
molecular dynamics of the most promising complexes of the protein-DNA  
complex and the ligand but do not know which force field to use.  
additionally how can i set up the parameters for the ligands?

any suggestions would be of great help

thanks in advance

greetings
joern